Historically, working with RNA derived from bacterial cells has been technically difficult because of its highly labile nature and the procedures used for its isolation. Early RNA extractions relied on guanidium isothiocyanate to lyse cells and denature proteins, while the RNA was isolated using a cesium chloride cushion and ultracentrifugation. Subsequently, the use of hot phenol replaced cesium gradients. However, RNA extractions using hot phenol had significant problems both due to the toxicity of the phenol and because the RNA obtained was not consistently of high quality. Accordingly, in the mid 1980s, a protocol was developed that included guanidium isothiocyanate and phenol, which yielded much more reproducible results compared to earlier methods.
Many companies have developed kits making it easier to isolate RNA. These kits, which are relatively expensive, vary greatly in the chemistry and/or mechanics used to lyse the cells, denature and remove proteins, and to isolate the RNA. For example, certain kits use detergents to aid cell lysis and capture RNA and DNA by precipitation. These current RNA isolation procedures contain multiple steps, leading to reduced sample recovery. Furthermore, current RNA isolation methods fail to provide an accurate representation of intracellular RNA pools, since each method appears to selectively enrich for either large or small RNAs relative to the levels of medium sized species. Thus depending on the isolation method used, certain size classes of RNA will be either enriched or depleted relative to the total RNA population.